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- PDB-2uy6: Crystal structure of the P pilus rod subunit PapA -

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Basic information

Entry
Database: PDB / ID: 2uy6
TitleCrystal structure of the P pilus rod subunit PapA
Components
  • PAP FIMBRIAL MAJOR PILIN PROTEIN
  • PERIPLASMID CHAPERONE PAPD PROTEIN
KeywordsCHAPERONE / DONOR STRAND COMPLEMENTATION / PILI/N-TERMINAL EXTENSION / PILUS BIOGENESIS / DONOR-STRAND EXCHANGE / NTE / DSC / DSE / PAPA / PAPD / FIMBRIA
Function / homology
Function and homology information


pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / extracellular region
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pap fimbrial major pilin protein / Periplasmid chaperone PapD protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVerger, D. / Bullitt, E. / Hultgren, S.J. / Waksman, G.
CitationJournal: Plos Pathog. / Year: 2007
Title: Crystal Structure of the P Pilus Rod Subunit Papa.
Authors: Verger, D. / Bullitt, E. / Hultgren, S.J. / Waksman, G.
History
DepositionApr 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMID CHAPERONE PAPD PROTEIN
B: PAP FIMBRIAL MAJOR PILIN PROTEIN
C: PAP FIMBRIAL MAJOR PILIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,8653
Polymers57,8653
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.100, 73.560, 80.480
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PERIPLASMID CHAPERONE PAPD PROTEIN


Mass: 24589.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HIS-TAGGED C TERMINUS / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2W9
#2: Protein PAP FIMBRIAL MAJOR PILIN PROTEIN / PAP PILI


Mass: 16637.451 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P04127
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLY 37 TO ASN ...ENGINEERED RESIDUE IN CHAIN B, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN B, THR 123 TO LEU ENGINEERED RESIDUE IN CHAIN C, THR 123 TO LEU
Sequence detailsSEQUENCE OF MATURE PROTEIN AFTER SIGNAL PEPTIDE CLIVAGE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.5 / Details: PEG8K 12%, 5% ISOPROPANOL, TRIS 0.1M PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→76.3 Å / Num. obs: 25542 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDK

1pdk


Resolution: 2.5→76.3 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE ARE 2 MOLECULES OF PAPA IN THE TERNARY COMPLEX (DA2). PAPA MOL B IS DONOR STRAND COMPLEMENTED BY PAPD, PAPA MOL C IS DONOR STRAND EXCHANGED BY PAPA MOL B
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 1300 5.1 %RANDOM
Rwork0.2219 ---
obs0.2219 25532 99.5 %-
Solvent computationBsol: 46.4546 Å2 / ksol: 0.362486 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.381 Å20 Å27.304 Å2
2---0.544 Å20 Å2
3---6.924 Å2
Refinement stepCycle: LAST / Resolution: 2.5→76.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 0 155 3895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006205
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30842
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.53 Å / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.345 --
Rwork0.329 863 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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